chr21-22826494-A-G

Variant names:

• chr21-22826494-A-G
• rs7279441

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.177 in 151,980 control chromosomes in the GnomAD database, including 2,736 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26785 AN: 151862 Hom.: 2725 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.177 AC: 26835 AN: 151980 Hom.: 2736 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74306

African (AFR) AF: 0.262 AC: 10860 AN: 41390

American (AMR) AF: 0.194 AC: 2961 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3468

East Asian (EAS) AF: 0.104 AC: 537 AN: 5172

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1365 AN: 10592

Middle Eastern (MID) AF: 0.210 AC: 60 AN: 286

European-Non Finnish (NFE) AF: 0.133 AC: 9028 AN: 67944

Other (OTH) AF: 0.186 AC: 393 AN: 2116

Alfa AF: 0.149 Hom.: 5044

Bravo AF: 0.184

Asia WGS AF: 0.181 AC: 626 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.65
PhyloP100		1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7279441; hg19: chr21-24198815;